This reverts commit c82770f5.

The shellcheck suggestion is spurious and results in SUBST_TOOLDIR being a
no-op. `set` sets positional arguments for bash, but we want to set the variable
given as the first autoconf argument.

Fixes #24542

Metric decreases because the paths in the settings file are now shorter,
so we allocate less when we read the settings file.

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Metric Decrease:
    T12425
    T13035
    T9198
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